| 1 | 17 | June-Reg | Brad Lidge | P | 21 | 6-5 | 200 | R | R | MLB | 2002-2009 | University of Notre Dame | $1,070,000 |
| 1 | 37 | June-Reg | Mike Nannini | P | 17 | 5-11 | 191 | R | R | AAA | | Green Valley (Henderson,NV) | $595,000 |
| 3 | 92** | June-Reg | Brad Busbin | P | 17 | 6-3 | 205 | R | R | A- | | Dr. Phillips (Orlando,FL) | |
| 4 | 122** | June-Reg | Jason Van Meetren | OF | 18 | 6-3 | 200 | R | R | A+ | | | |
| 5 | 152 | June-Reg | Scott Barrett | P | 19 | 5-10 | 175 | L | L | A- | | San Jacinto College | |
| 6 | 182 | June-Reg | Dave Matranga | IF | 21 | 6-0 | 163 | R | R | MLB | 2003-2005 | Pepperdine University | |
| 7 | 212 | June-Reg | John Buck | C | 17 | 6-3 | 210 | R | R | MLB | 2004-2009 | Taylorsville (Salt Lake City,UT) | |
| 8 | 242 | June-Reg | Jesse Joyce | 3B | 22 | 5-10 | 185 | R | R | A+ | | Cal State Los Angeles | |
| 9 | 272 | June-Reg | Morgan Ensberg | 3B | 22 | 6-2 | 210 | R | R | MLB | 2000-2008 | USC | |
| 10 | 302 | June-Reg | Keith Ginter | 2B | 22 | 5-10 | 190 | R | R | MLB | 2000-2005 | Texas Tech University | |
| 11 | 332** | June-Reg | Kevin Jordan | | 21 | 6-1 | 190 | R | R | A+ | | Texas Tech University | |
| 12 | 362 | June-Reg | Jeremy Ryan | P | 20 | 6-4 | 195 | R | R | A | | | |
| 13 | 392 | June-Reg | Doug Sessions | P | 21 | 6-1 | 209 | R | R | AAA | | Armstrong (Savannah,GA) | |
| 14 | 422** | June-Reg | Jacob Baker | | 22 | 6-3 | 220 | R | R | A | | Rice University | |
| 15 | 452 | June-Reg | Chuck Carter | 1B | | | 0 | | | - | | Baylor University | |
| 16 | 482 | June-Reg | Derek Nicholson | OF | 22 | 6-0 | 200 | L | R | AAA | | University of Florida | |
| 17 | 512 | June-Reg | Colin Porter | OF | 22 | 6-2 | 200 | L | L | MLB | 2003-2004 | University of Arizona | |
| 18 | 542 | June-Reg | Rich Terwilliger | P | 19 | 6-3 | 180 | R | R | A- | | Finger Lakes (Corning,NY) | |
| 19 | 572 | June-Reg | Byron Wilkerson | P | 21 | 6-3 | 205 | R | R | A+ | | University of Mary Hardin-Baylor | |
| 20 | 602 | June-Reg | Anthony Ramirez | 3B | 17 | 6-1 | 200 | L | R | Rookie | | Carson (Carson,CA) | |
| 21 | 632** | June-Reg | Brian Messer | P | 21 | 6-4 | 208 | R | R | A | | University of New Mexico | |
| 22 | 662 | June-Reg | Garrett Zyskowski | P | 22 | 6-1 | 185 | L | L | A | | West Virginia University | |
| 23 | 692 | June-Reg | Brandon Smith | P | 22 | 6-1 | 205 | R | R | A | | University of Louisiana-Monroe | |
| 24 | 722 | June-Reg | Joshua Dimmick | C | 22 | 6-3 | 225 | B | R | A | | University of Kansas | |
| 25 | 752 | June-Reg | Jacob Whitney | P | 22 | 6-2 | 220 | L | L | A+ | | Iowa State University | |
| 26 | 782 | June-Reg | Robert Carrillo | 1B | 19 | 6-6 | 260 | R | R | A- | | Montgomery (San Diego,CA) | |
| 27 | 812 | June-Reg | Bobby Burns | | | | | | | College | | Bingham (South Jordan,UT) | |
| 28 | 842** | June-Reg | Chris Sheffield | P | 18 | 6-3 | 215 | R | R | A- | | Stephen F. Austin University | |
| 29 | 872 | June-Reg | Brandon Buckley | C | 21 | 6-2 | 205 | R | R | AA | | Texas Tech University | |
| 30 | 902** | June-Reg | Jordan Hunt | P | 19 | 6-4 | 195 | R | R | Rookie | | | |
| 31 | 932** | June-Reg | Alex Dvorsky | C | 18 | 6-2 | 195 | R | R | A | | Marion (Marion,LA) | |
| 32 | 962** | June-Reg | Bernie Gonzalez | OF | 18 | 6-2 | 205 | R | R | A+ | | | |
| 33 | 992 | June-Reg | Gavin Wright | OF | 19 | 6-2 | 175 | R | R | AA | | Blinn College | |
| 35 | 1052** | June-Reg | Brett Kay | C | 18 | 6-1 | 190 | R | R | A+ | | Mater Dei (Santa Ana,CA) | |
| 36 | 1082 | June-Reg | Benson Barrera | | | | | | | College | | Skyview (Nampa,ID) | |
| 37 | 1112** | June-Reg | Jeremy Frost | C | 18 | 6-3 | 210 | R | R | AA | | Oviedo (Oviedo,FL) | |
| 38 | 1142** | June-Reg | Bryan Edwards | P | 18 | 5-11 | 170 | R | R | AA | | Northeast Texas Community College | |
| 39 | 1172 | June-Reg | Roberto Zaldivar | | 18 | 6-3 | 195 | R | R | College | | Arroyo (San Lorenzo,CA) | |
| 40 | 1202** | June-Reg | Ray Leyba | P | | | 0 | | | - | | Choctaw (Choctaw,OK) | |
| 41 | 1232 | June-Reg | Mike McHugh | P | 25 | 5-11 | 180 | L | L | A+ | | Helix Charter (La Mesa,CA) | |